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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctgaacttgcttgtggattatagatgcttttgttattattagctctgaaataatgctcattattacaatgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG

Basic information

species Zea mays
transcript GRMZM2G177276_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
---------------------------------------gtaagttctgaacttgcttgtggattatagatgcttttgttattattagctctgaaataatgctcatta--------ttacaatgtttt-gcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
                                       | ||| | | | |  |      ||||||   | ||||| |  ||| |   | ||||| |||   ||| |        |||  ||||||| ||||||||||| |||||||||||||| ||||||||||| |||||
gtaagttaatatgatcatattttttttactttattatatgcaaggttt-atcccgtgatcagattatgattacttttatatttaatgatt-tgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG

upper sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
gtaagttctgaacttgcttgtggattatagatgcttttgttattattagctctgaaataatgctcattatt-----acaatgt------tttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
|||||||||    |   |||| |   | |     |  | | || | |    |   | ||    | | ||||     || || |      |||||||||||||| |||  ||||||||| |||||||||||  ||||
gtaagttctcttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 6
gtaagttctgaacttgcttgtggattatagatgcttttgttattattagctctgaaataatgctcattattacaatg-----------ttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
||||| | |    |   |||| |   | |     |  | | || | || | |   | ||    | | |||| |   |           ||||||||||||||| |||  ||||||||| |||||||||||  ||||
gtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaaccc-atattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
-----gtaagttctgaacttgcttgtggattatagatgcttttgttattattagctctgaaataatgctcattattacaatg-----------ttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
     ||||| | |    |   |||| |   | |     |  | | || | || | |   | ||    | | |||| |   |           ||||||||||||||| |||  ||||||||| |||||||||||  ||||
tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaaccc-atattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------------------------gtaagttctgaacttgcttgtggattatagatgcttttgttattatta----gctctgaaataatgctcattattacaatgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
                                                                                                               |   || |   | | | |||||| | | | || || || |    |      |  ||||    |||      ||   ||||  || |||||||||| ||  ||||||||||||||||||||||| ||||
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttg-tgtttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60399873|gb|DN232683.1|DN232683
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|37388163|gb|CF631288.1|CF631288
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|18163947|gb|BM333786.1|BM333786
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|78025971|gb|DV494358.1|DV494358
EST:     TAGCGGCAGTTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCTTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|211489813|gb|FL245176.1|FL245176
EST:     AGCGGCAGATTTGCGCCACATAAAAGAATATGCTTTGTCA-TGAGTGACT                         TTCATCCTGAATCTTGNAAATCCA-TGTGGTCTGTTGCAAGCATTCTCAC
genomic: AGCGGCAGGTTTGCGCCACATAAAAGAATATGCTT-GTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAA-TCCAATGTGGTCTGTTGCAAGCATTCTCAC
EST: gi|60347014|gb|DN213987.1|DN213987
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|32945073|gb|CF049892.1|CF049892
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|32943110|gb|CF047929.1|CF047929
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATACGCTTGTCAATAAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|37396958|gb|CF635773.1|CF635773
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|33942242|gb|CF348842.1|CF348842
EST:     CGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCCTGGAATCCAATGTGGTCTGTTGCAAG
genomic: CGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|16922843|gb|BM075835.1|BM075835
EST:     GCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: GCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|31355568|gb|CD439925.1|CD439925
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|76925873|gb|DV170631.1|DV170631
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|78120786|gb|DV539170.1|DV539170
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|76925875|gb|DV170632.1|DV170632
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|78120787|gb|DV539171.1|DV539171
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
EST: gi|33103288|gb|CF063248.1|CF063248
EST:     TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
genomic: TAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 184

CATGACAACCCCTAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 130

CATGACAACCCCTAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 167

CATGACAACCCCTAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 150

CATGACAACCCCTAGCGGCAGGTTTGCGCCACATAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... tgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttttgttattattagctctgaaataatgctcattattacaatgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
                                   attattacaatgtttt  TA-rich tract